2FR3

Crystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.131 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.

Vaezeslami, S.Mathes, E.Vasileiou, C.Borhan, B.Geiger, J.H.

(2006) J Mol Biol 363: 687-701

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.059
  • Primary Citation of Related Structures:  
    2FR3, 2FRS, 2FS6, 2FS7

  • PubMed Abstract: 

    CRABPII is a small, cytosolic protein that solubilizes and transfers retinoic acid (RA) to the nucleus while also enhancing its transcriptional activity. We have determined the first high-resolution structure of apo-wild type (WT) CRABPII at 1.35 A. Using three different data sets collected on apo-WT CRABPII we have shown that apo- and holo-CRABPII share very similar structures. Binding of RA appears to increase the overall rigidity of the structure, although the induced structural changes are not as pronounced as previously thought. The enhanced structural rigidity may be an important determinant for the enhanced nuclear localization of the RA-bound protein. Comparison of our apo-WT with a mutant apo-CRABPII structure shows that mutation of Arg111, a conserved residue of CRABPII and a key residue in RA binding, causes structural changes in the molecule. We further investigated the structural importance of conserved residues by determining the structure of the F15W mutant CRABPII (F15W-CRABPII). Our structures also demonstrate structural changes induced by crystal packing and show that a crystal can harbor demonstrative structural differences in the asymmetric unit.


  • Organizational Affiliation

    Chemistry Department, Michigan State University, East Lansing, MI 48824-1322, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid binding protein 2137Homo sapiensMutation(s): 0 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
GTEx:  ENSG00000143320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
REA Binding MOAD:  2FR3 Kd: 2 (nM) from 1 assay(s)
BindingDB:  2FR3 Kd: 200 (nM) from 1 assay(s)
PDBBind:  2FR3 Kd: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.287α = 90
b = 46.464β = 90
c = 77.261γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations